Development of global consensus sequence of HCV glycoproteins involved in viral entry
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RESEARCH
Open Access
Development of global consensus sequence of HCV glycoproteins involved in viral entry Sobia Idrees1*, Usman A Ashfaq1 and Natasha Idrees2 * Correspondence: [email protected] 1 Department of Bioinformatics and Biotechnology, Government College University (GCU), Faisalabad, Pakistan Full list of author information is available at the end of the article
Abstract Background: HCV affects >170 million people worldwide and is a leading cause of liver diseases such as hepatocellular carcinoma. Each year, Pakistan reports hundreds of cases and now it has become a serious health issue. HCV has two transmembrane glycoproteins (E1 and E2) that are involved in virus entry through viral attachment, but because of their hypervariable nature they have become difficult targets for vaccine development. Methods: A total of 150 protein sequences of E1 and E2 belonging to genotypes 3a and 1a were retrieved from the NCBI protein database and were subjected to conservation and variation analysis using the multiple sequence alignment feature of the CLC workbench. A consensus sequence of each genotype of E1 and E2 was obtained and these consensus sequences were further analyzed to construct a global consensus sequence, which was used to design potentially conserved peptides. Results: From the sequence conservation analysis, highly conserved residues were identified and were used to design peptides. Only two peptides were found to be conserved in the E1 protein of genotypes 3a and 1a and a total of nine conserved peptides were designed for the HCV E2 protein of those genotypes. These designed peptides could serve as useful targets in developing new inhibitory compounds. Conclusion: This study was designed to perform conservation and variability analysis of HCV glycoproteins and to find potentially conserved peptides among genotypes 3a and 1a (the most prevalent genotypes in Pakistan) that could serve as useful targets in the development of novel inhibitory compounds, thus reducing the threat of HCV infection in Pakistan. Keywords: HCV, Glycoproteins, Conservation, Peptides
Background Chronic infection with hepatitis C virus (HCV) affects >170 million individuals, approximately 3% of the world population, and is responsible for approximately 350,000 deaths every year [1]. HCV has become a leading cause of liver diseases such as hepatocellular carcinoma. It is a small, single-stranded, positive strand RNA virus encoding structural and non-structural proteins. It has many genetic variants, an important factor to consider in drug development. There are six known major genotypes and >100 subtypes of HCV [1,2] and owing to this strain variability, no vaccine has been developed to date; the currently approved treatment for HCV is pegylated interferon α (PEG-INF α) in combination with ribavirin and Boceprevir/Telaprevir. © 2013 Idrees et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which
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